Looking at the photos in Marriot's "Royal Navy Frigates 1945 - 1983", I think the original funnel stucture was actually much the same height as the later funnel - then the domed top added height, and a slight rake was introduced.
According to Marriot Scarborough retained her original funnel for "most of her active life".

For my Scarborough, I've taken a file to a Triang Whitby, and flattened the "dome". Not 100% accurate, but not out of kilter with the rest of the model.